Is PPCS p.Arg29= (c.85A>C) pathogenic?

PPCS p.Arg29= (c.85A>C) is classified Likely benign in PPCS (ClinVar, Single submitter, 1 submitter; last evaluated 2023-09-14). Absent from gnomAD v4.1.

How common is PPCS p.Arg29= (c.85A>C) in the general population?

PPCS p.Arg29= (c.85A>C) is absent from gnomAD v4.1 (gnomAD).

PPCS p.Arg29=

c.85A>C · rs889389908 · VCV2845538

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,590,512)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.1	GERP -4.3
Overall
CADD	5.205	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,590,512). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: PPCS
Protein: p.Arg29=
Coding: c.85A>C
MANE Select: NM_024664
dbSNP: rs889389908
Type: single nucleotide variant
Location: chr1:42456650 (GRCh38)
Gene constraint: LOEUF 1.064 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.94 · 2 PDB
Residue 29: an α-helix

Full PPCS gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PPCS p.Ala162Pro Uncertain significance ★★ ⚠ same type
PPCS p.Pro107Ser Uncertain significance ★★ ⚠ same type
PPCS c.*91T>G Benign ★★ same type
PPCS p.Leu280= Benign/Likely benign ★★ same type
PPCS p.Phe73= Likely benign ★★ same type
PPCS p.Ala8Ser Uncertain significance ★ ⚠ same type
PPCS p.Leu118Met Uncertain significance ★ ⚠ same type
PPCS p.Thr68Pro Uncertain significance ★ ⚠ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/ppcs-p-arg29 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown